chore: change logs location

matinnuhamunada · Mar 13, 2024 · 92f2970 · 92f2970
1 parent a03a8a3
commit 92f2970
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Showing 3 changed files with 19 additions and 19 deletions.
diff --git a/workflow/rules/01_trycycler_assembly.smk b/workflow/rules/01_trycycler_assembly.smk
@@ -7,7 +7,7 @@ rule clean_nanopore:
         "../envs/utilities.yaml"
     threads: 4
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/clean_nanopore-{strains}.log"
+        "logs/01_trycycler_assembly/{strains}/clean_nanopore-{strains}.log"
     shell:
         """
         porechop -t {threads} -i {input} -o {output} &>> {log}
@@ -21,7 +21,7 @@ rule filter_length:
     conda:
         "../envs/utilities.yaml"
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/filter_length-{strains}.log"
+        "logs/01_trycycler_assembly/{strains}/filter_length-{strains}.log"
     params:
         min_length = 1000,
         keep_percent = 95
@@ -37,7 +37,7 @@ rule subsample:
         temp(expand('data/interim/01_trycycler_assembly/{{strains}}/nanopore/read_subsets/sample_{subsample}.fastq', subsample=['01', '02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12']))
     threads: 12
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/subsample-{strains}.log"
+        "logs/01_trycycler_assembly/{strains}/subsample-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     params:
@@ -57,7 +57,7 @@ rule assemble_flye:
         graph = 'data/interim/01_trycycler_assembly/{strains}/nanopore/assemblies/assembly_{subsample}.gfa',
     threads: 8
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/assemble_flye/assemble_flye-{strains}_{subsample}.log"
+        "logs/01_trycycler_assembly/{strains}/assemble_flye/assemble_flye-{strains}_{subsample}.log"
     wildcard_constraints:
         subsample="|".join(['01', '04', '07', '10']),
     conda:
@@ -77,7 +77,7 @@ rule assemble_minipolish:
         graph = 'data/interim/01_trycycler_assembly/{strains}/nanopore/assemblies/assembly_{subsample}.gfa'
     threads: 8
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/assemble_minipolish/assemble_minipolish-{strains}_{subsample}.log"
+        "logs/01_trycycler_assembly/{strains}/assemble_minipolish/assemble_minipolish-{strains}_{subsample}.log"
     wildcard_constraints:
         subsample="|".join(['02', '05', '08', '11']),
     conda:
@@ -112,7 +112,7 @@ rule assemble_raven:
         graph = 'data/interim/01_trycycler_assembly/{strains}/nanopore/assemblies/assembly_{subsample}.gfa'
     threads: 8
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/assemble_raven/assemble_raven-{strains}_{subsample}.log"
+        "logs/01_trycycler_assembly/{strains}/assemble_raven/assemble_raven-{strains}_{subsample}.log"
     wildcard_constraints:
         subsample="|".join(['03', '06', '09', '12']),
     conda:
@@ -129,7 +129,7 @@ rule draw_graph:
         graph = temp('data/processed/{strains}/01_trycycler_assembly/{subsample}_{strains}.png'),
         gfa = 'data/processed/{strains}/01_trycycler_assembly/{strains}_{subsample}.gfa'
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/bandage/{strains}_{subsample}.log"
+        "logs/01_trycycler_assembly/{strains}/bandage/{strains}_{subsample}.log"
     conda:
         "../envs/utilities.yaml"
     shell:
@@ -144,7 +144,7 @@ rule merge_draw_graph:
     output:
         png = "data/processed/{strains}/01_trycycler_assembly/{strains}_graphs.png",
     log:
-        "workflow/report/logs/01_trycycler_assembly/{strains}/bandage/merge_{strains}.log"
+        "logs/01_trycycler_assembly/{strains}/bandage/merge_{strains}.log"
     conda:
         "../envs/utilities.yaml"
     params:

diff --git a/workflow/rules/02_trycycler_cluster.smk b/workflow/rules/02_trycycler_cluster.smk
@@ -6,7 +6,7 @@ rule trycycler_cluster:
         cluster=directory('data/interim/02_trycycler_cluster/{strains}')
     threads: 12
     log:
-        "workflow/report/logs/02_trycycler_cluster/trycycler_cluster/02_trycycler_cluster-{strains}.log"
+        "logs/02_trycycler_cluster/trycycler_cluster/02_trycycler_cluster-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     shell:  
@@ -20,7 +20,7 @@ rule cluster_dump:
     output:
         yaml = 'data/interim/02_trycycler_cluster/cluster.yaml'
     log:
-        "workflow/report/logs/02_trycycler_cluster/cluster_dump/cluster_dump.log"
+        "logs/02_trycycler_cluster/cluster_dump/cluster_dump.log"
     params:
         cluster_path = 'data/interim/02_trycycler_cluster'
     run:
@@ -49,7 +49,7 @@ rule cluster_draw:
     output:
         png = 'data/processed/{strains}/02_trycycler_cluster/{strains}_cluster.png'
     log:
-        "workflow/report/logs/02_trycycler_cluster/cluster_draw/draw_cluster_{strains}.log"
+        "logs/02_trycycler_cluster/cluster_draw/draw_cluster_{strains}.log"
     conda:
         "../envs/R.yaml"
     shell:

diff --git a/workflow/rules/03_trycycler_consensus.smk b/workflow/rules/03_trycycler_consensus.smk
@@ -5,7 +5,7 @@ rule trycycler_intermediate:
         reconcile = 'data/interim/03_trycycler_consensus/{strains}/{cluster}_copy.log'
     threads: 1
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_intermediate/trycycler_intermediate-{cluster}-{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_intermediate/trycycler_intermediate-{cluster}-{strains}.log"
     params:
         cluster_file = config["clusters"]
     shell:  
@@ -21,7 +21,7 @@ rule trycycler_reconcile:
         reconcile = 'data/interim/03_trycycler_consensus/{strains}/{cluster}/2_all_seqs.fasta'
     threads: 8
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_reconcile/trycycler_reconcile-{cluster}-{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_reconcile/trycycler_reconcile-{cluster}-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     params:
@@ -39,7 +39,7 @@ rule trycycler_MSA:
         msa = 'data/interim/03_trycycler_consensus/{strains}/{cluster}/3_msa.fasta'
     threads: 8
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_MSA/trycycler_MSA-{cluster}-{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_MSA/trycycler_MSA-{cluster}-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     params:
@@ -58,7 +58,7 @@ rule trycycler_partition:
         partition = "data/interim/03_trycycler_consensus/{strains}/partition.log"
     threads: 8
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_partition/trycycler_partition_{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_partition/trycycler_partition_{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     params:
@@ -77,7 +77,7 @@ rule trycycler_consensus:
         consensus = 'data/interim/03_trycycler_consensus/{strains}/{cluster}/7_final_consensus.fasta'
     threads: 8
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_consensus/trycycler_consensus-{cluster}-{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_consensus/trycycler_consensus-{cluster}-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     shell:  
@@ -94,7 +94,7 @@ rule medaka_polish:
         "../envs/trycycler.yaml"
     threads: 8
     log:
-        "workflow/report/logs/03_trycycler_consensus/medaka_polish/medaka_polish-{cluster}-{strains}.log"
+        "logs/03_trycycler_consensus/medaka_polish/medaka_polish-{cluster}-{strains}.log"
     params:
         model = 'r941_min_sup_g507',
         cluster = "data/interim/03_trycycler_consensus/{strains}/{cluster}",
@@ -112,7 +112,7 @@ rule trycycler_concat:
         assembly = 'data/interim/03_trycycler_consensus/{strains}/assembly.fasta'
     threads: 1
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_concat/trycycler_concat-{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_concat/trycycler_concat-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     shell:  
@@ -127,7 +127,7 @@ rule format_final_assembly:
         assembly = 'data/processed/{strains}/03_trycycler_consensus/{strains}.fna'
     threads: 1
     log:
-        "workflow/report/logs/03_trycycler_consensus/trycycler_format_final_assembly/trycycler_format_final_assembly-{strains}.log"
+        "logs/03_trycycler_consensus/trycycler_format_final_assembly/trycycler_format_final_assembly-{strains}.log"
     conda:
         "../envs/trycycler.yaml"
     shell: